scholarly journals ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Eunsoo Lee ◽  
Jungyoon Choi ◽  
Youhwa Jo ◽  
Joo Yeon Kim ◽  
Yu Jin Jang ◽  
...  
Keyword(s):  
Fluorescent Proteins ◽  
Three Dimensional ◽  
Cellular Level ◽  
Whole Body ◽  
Dimensional Structure ◽  
Entire Body ◽  
Tissue Architecture ◽  
Tissue Clearing ◽  
3 Dimensional ◽  
Labeling Method

Abstract Understanding the structural organization of organs and organisms at the cellular level is a fundamental challenge in biology. This task has been approached by reconstructing three-dimensional structure from images taken from serially sectioned tissues, which is not only labor-intensive and time-consuming but also error-prone. Recent advances in tissue clearing techniques allow visualization of cellular structures and neural networks inside of unsectioned whole tissues or the entire body. However, currently available protocols require long process times. Here, we present the rapid and highly reproducible ACT-PRESTO (active clarity technique-pressure related efficient and stable transfer of macromolecules into organs) method that clears tissues or the whole body within 1 day while preserving tissue architecture and protein-based signals derived from endogenous fluorescent proteins. Moreover, ACT-PRESTO is compatible with conventional immunolabeling methods and expedites antibody penetration into thick specimens by applying pressure. The speed and consistency of this method will allow high-content mapping and analysis of normal and pathological features in intact organs and bodies.

Three-Dimensional Reconstruction Using Stereo Pairs from Serial Thick Sections

1977 ◽  
Vol 35 ◽  
pp. 562-563
Author(s):  
Robert Glaeser ◽  
Thomas Bauer ◽  
David Grano
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Thin Sections ◽  
3 Dimensional ◽  
Transmission Electron ◽  
Freeze Dried ◽  
Dimensional Reconstruction ◽  
Stereo Imagery ◽  
Whole Mounts

In transmission electron microscopy, the 3-dimensional structure of an object is usually obtained in one of two ways. For objects which can be included in one specimen, as for example with elements included in freeze- dried whole mounts and examined with a high voltage microscope, stereo pairs can be obtained which exhibit the 3-D structure of the element. For objects which can not be included in one specimen, the 3-D shape is obtained by reconstruction from serial sections. However, without stereo imagery, only detail which remains constant within the thickness of the section can be used in the reconstruction; consequently, the choice is between a low resolution reconstruction using a few thick sections and a better resolution reconstruction using many thin sections, generally a tedious chore. This paper describes an approach to 3-D reconstruction which uses stereo images of serial thick sections to reconstruct an object including detail which changes within the depth of an individual thick section.

scholarly journals EZ Clear for simple, rapid, and robust mouse whole organ clearing

2022 ◽  
Author(s):  
Chih-Wei Hsu ◽  
Juan Cerda ◽  
Jason M Kirk ◽  
Williamson D. Turner ◽  
Tara L. Rasmussen ◽  
...  
Keyword(s):  
Biomedical Research ◽  
Room Temperature ◽  
Adult Mouse ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Fluorescence Signal ◽  
Tissue Architecture ◽  
Tissue Clearing ◽  
Clearing Method ◽  
Three Dimensional Space

Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevents the widespread adoption of these methods. Here we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hours in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, EZ Cleared samples can be further processed for downstream embedding and cryosectioning followed by standard histology or immunostaining, without loss of endogenous or synthetic fluorescence signal. Overall, the simplicity, speed, and flexibility of EZ Clear make it easy to adopt and apply to diverse approaches in biomedical research.

Three dimensional structure of the leishmania amastigote as revealed by computer-aided reconstruction from serial sections

Parasitology ◽  
1986 ◽  
Vol 92 (1) ◽  
pp. 13-23 ◽  
Author(s):  
G. H. Coombs ◽  
L. Tetley ◽  
V. A. Moss ◽  
K. Vickerman
Keyword(s):  
Cell Volume ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Serial Sections ◽  
Leishmania Mexicana ◽  
Cell Organelles ◽  
3 Dimensional ◽  
Computer Aided ◽  
Total Cell Volume

SUMMARYComputer-aided reconstruction from serial sections has been used to analyse the 3-dimensional structure of entire amastigotes of Leishmania mexicana mexicana and to determine the number, arrangement and volume of each organelle. In two reconstructions, the lysosome-like ‘megasomes’ were the most numerous organelle, there being 34 in one amastigote, and they comprised as much as 15% of the total cell volume. In contrast, as few as 9 glycosomes were present, accounting for less than 1% of the cell volume. The unitary nature of the mitochondrion was confirmed and its complex basket-like structure was revealed. The spatial arrangement of the cell organelles is here displayed in stereo-pairs.

Clinical use of a three-dimensional tissue marker to target postlumpectomy radiation.

2015 ◽  
Vol 33 (28_suppl) ◽  
pp. 53-53 ◽  
Author(s):  
Cary Steven Kaufman ◽  
William H. Hall ◽  
Greg M Wolgamot ◽  
Laurie Hill ◽  
Rebecca Caro ◽  
...  
Keyword(s):  
Radiation Therapy ◽  
Three Dimensional ◽  
National Registry ◽  
Clinical Findings ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Cancer Management ◽  
Pathologic Findings ◽  
Tissue Marker ◽  
One Year

53 Background: A three dimensional bioabsorbable coiled tissue marker has been developed to facilitate targeting for radiation therapy post lumpectomy. Proposed advantages are a) clarified targeting of closest margins to the excised tumor, b) providing a three dimensional structure that allows fibrosis to add volume to contribute to cosmesis, c) aiding in re-excision localization. Our experience has demonstrated the array of clinical findings after placement, the imaging findings over time, and pathologic findings for early and late removal. Methods: Consecutive lumpectomy patients who were candidates for targeted radiation therapy were implanted with the 3-D bioabsorbable marker from May 2014 to June 2015. After informed consent, each of 36 patients were followed to gather clinical, imaging and pathologic findings. Standard breast cancer management decisions were made (NCCN). Patients requiring re-excision were examined for pathologic findings related to the device. Routine imaging with mammography and ultrasound were obtained at 6 and 12 months post lumpectomy. Results: The use of the spiral tissue marker with the fixed array of six titanium clips provided a predictable target for radiation treatments. As the tissue marker was sewn to the closest tumor bed, inadvertent dissection planes caused by oncoplastic techniques could be avoided. Clinically the lumpectomy site was firm/dense in 94% of patients at 3 months (n = 36), but in only 60% at one year (n = 21). Two patients who underwent re-excision for positive margins were guided by the 3-dimensional device. Two patients had removal at one month and at 12 months for reasons unrelated to the tissue marker. Histologic examination demonstrated typical foreign body reaction and organization (fig 1b). Mammography at one year demonstrated marker clips coalescing as the bioabsorbable device dissolves with maintenance of the volume of the cavity in 50% of patients(fig 1c). Cosmetic outcome has been good to excellent measured at 6 and 12 months. Conclusions: Clinical, radiologic and pathologic findings during use of a novel bioabsorbable 3-dimensional tissue marker were presented. A national registry to further define these attributes will soon be started.

scholarly journals Nanoparticles Mediated Protein Stability in Comparison with Osmolytes: in vivo Approach

2021 ◽  
Vol 33 (6) ◽  
pp. 1433-1438
Author(s):  
R. Verma ◽  
N. Singh ◽  
P. Chaudhuri (Chattopadhyay)
Keyword(s):  
Gold Nanoparticles ◽  
Dihydrofolate Reductase ◽  
Three Dimensional ◽  
Cellular Level ◽  
Dimensional Structure ◽  
Important Group ◽  
Unfolded State ◽  
The Status ◽  
The Stability

The native three-dimensional structure of protein is quite unstable under critical destabilizing conditions. In order to enhance the stability and activity for a proper folded environment of a protein, many stabilizing materials are added such as nanoparticles and osmolytes to an unfolded state of protein. Osmolytes are the important group of molecules which are engaged by the cell as an adaption in the severe conditions. In this communication, a comparative in vivo study is reported for imparting the status of stability and folding ability of zebrafish dihydrofolate reductase (zDHFR) protein with gold nanoparticles and various osmolytes (glycerol, glucose and betain). Present observations revealed that the interaction of gold nanoparticles (AuNPs) with bacteria at the cellular level helps in maintaining the stability of protein more effectively than osmolytes which could be used for many biological and pharmacological approaches although glycerol as an osmolyte also stabilizes the protein at a significant level.

Imaging, representation and analysis of 3-dimensional biological structures by confocal microscopy

1988 ◽  
Vol 46 ◽  
pp. 996-997
Author(s):  
G.J. Brakenhoff ◽  
H.T.M. van der Voort
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Confocal Scanning Laser Microscopy ◽  
Optical Sectioning ◽  
Basic Aspect ◽  
3 Dimensional ◽  
Scanning Laser Microscopy ◽  
Confocal Scanning ◽  
Confocal Scanning Laser ◽  
A New Technique

Confocal scanning laser microscopy is a new technique capable of visualizing the three-dimensional structure in suitable objects. As further explained in fig. 1 the basic aspect of this type of microscopy is that one and the same object point in the specimen is both optimally illuminated from a laser illuminated pinhole as well as optimally imaged on a detector pinhole. Due to the specific properties of this optical arrangement not only the lateral resolution is substantially improved, but also an excellent optical sectioning property comes available. The latter means that only information from a chosen plane in the specimen will contribute to the image, while the influence of the layers above and below is suppressed. The important advantage over elec- tronmicroscopy, apart from the speed of the technique, is that to make the 3-D information accessible in a specimen no mechanical sectioning of the material is necessary.

New Insights Into the Three-Dimensional Structure of the Nucleus and Chromosomes

1997 ◽  
Vol 3 (S2) ◽  
pp. 213-214
Author(s):  
J. Sedat ◽  
W. Marshall ◽  
A. Dernburg ◽  
J. Fung ◽  
D. Agard
Keyword(s):  
Chromosome Structure ◽  
Position Effect ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Position Effect Variegation ◽  
Genetic Loci ◽  
Interphase Nuclei ◽  
Intact Cells ◽  
3 Dimensional ◽  
Specific Localization

Recent methodology, to be described, now makes possible specific localization and analysis of genetic loci within 3-Dimensional interphase nuclei in intact cells and tissues with minimal perturbation of the chromosome structure (Dernburg and Sedat, 1997). These techniques define genetic loci that specifically interact with the nuclear envelope and interior structures; we are able to map all loci to highly localized 3-dimensional positions within Drosophila embryonic nuclei (Marshall et al, 1996). S-Dimensions-as-a-function-of-time (4-D) studies of live nuclei, from Yeast and Drosophila, allow dynamic chromosome interactions to be probed and quantitated. Our results suggest a very dynamic but highly determined and organized nucleus. Using these approaches, we can now study specific mechanisms leading to homologue chromosome pairing and position-effect variegation (Dernburg et al., 1996).

scholarly journals The 3-dimensional structure of NGC 891 and M51

2011 ◽  
Vol 7 (S284) ◽  
pp. 104-106
Author(s):  
Andrew Schechtman-Rook ◽  
Matthew A. Bershady ◽  
Kenneth Wood ◽  
Thomas P. Robitaille
Keyword(s):  
Monte Carlo ◽  
Spiral Structure ◽  
Scattered Light ◽  
Three Dimensional ◽  
Major Axis ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
The Galaxy ◽  
Color Gradient ◽  
3D Monte Carlo

AbstractWe investigate the three-dimensional structure of the nearby edge-on spiral galaxy NGC 891 using 3D Monte Carlo radiative transfer models, with realistic spiral structure and fractally clumped dust. Using the spiral and clumpiness parameters found from recently completed scattered light models we produce lower resolution SED models which reproduce the spatially-integrated UV-to-FIR SED of NGC 891. Our models contain a color gradient across the major axis of the galaxy - similar to what is seen in images of the NGC 891. With minor adjustment our SED models are able to match the SED of M51, a similar galaxy at a near face-on inclination.

Three-dimensional Structure of Twinned and Zigzagged One-dimensional Nanostructures Using Electron Tomography

2010 ◽  
Vol 1262 ◽  
Author(s):  
Han Sung Kim ◽  
Yoon Myung ◽  
Yong Jae Cho ◽  
Dong Myung Jang ◽  
Chan Soo Jung ◽  
...  
Keyword(s):  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Axial Direction ◽  
Zone Axis ◽  
Dimensional Structure ◽  
3 Dimensional ◽  
Superlattice Structure ◽  
Transmission Electron ◽  
Inas Nanowires

AbstractElectron tomography and high-resolution transmission electron microscopy were used to characterize the unique 3-dimensional (3D) structures of twinned Zn3P2 (tetragonal) and InAs (zinc blende) nanowires synthesized by the vapor transport method. The Zn3P2 nanowires adopt a unique superlattice structure that consists of twinned octahedral slice segments having alternating orientations along the axial [111] direction of a pseudocubic unit cell. The apices of the octahedral slice segment are indexed as six equivalent <112> directions at the [111] zone axis. At each 30 degrees turn, the straight and zigzagged morphologies appear repeatedly at the <112> and <011> zone axes, respectively. The 3D structure of the twinned Zn3P2 nanowires is virtually the same as that of the twinned InAs nanowires. In addition, we analyzed the 3D structure of zigzagged CdO (rock salt) nanowires and found that they include hexahedral segments, whose six apices are matched to the <011> directions, linked along the [111] axial direction. We also analyzed the unique 3D structure of rutile TiO2 (tetragonal) nanobelts; at each 90 degree turn, the straight morphology appears repeatedly, while the in-between twisted form appears at the [011] zone axis. We suggest that the TiO2 nanobelts consist of twinned octahedral slices whose six apices are indexed by the <011>/<001> directions with the axial [010] direction.

scholarly journals 3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

2021 ◽  
Vol 12 (2) ◽  
pp. 85
Author(s):  
Tina Zarkiyani ◽  
I Made Budiarsa ◽  
Astija Astija ◽  
Mursito S Bialangi
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Columba Livia ◽  
Dimensional Structure ◽  
Structural Quality ◽  
Three Dimensional Structure ◽  
3 Dimensional ◽  
Access Code ◽  
Development And Differentiation

The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.

Sign in / Sign up

Export Citation Format

Share Document